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        <title>Optimization - Optimize fluxes</title>
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        <h1>Optimize fluxes module</h1>
        <h2>Description</h2>
        <p>
            This module is using the R package sybil (<a href="http://cran.r-project.org/web/packages/sybil/sybil.pdf">http://cran.r-project.org/web/packages/sybil/sybil.pdf</a>)
            to perform the FBA (Flux Balance Analysis) on the selected model. The R function is written in the folder "conf" of this 
            program. The name of the file is "FBA.R" and can be edited by the user. Only the arguments of the function and the returning variables must be 
            respected. The fluxes are minimized in the same R function.
        </p>        
        <p>
            Check the instructions about how to integrated R with this program in the main help page.
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        <p>   
            The output is a SBML file containing the reactions that have fluxes different than zero. A flux threshold will be added in the next version of the 
            program to decide what reactions must be included in the resulting model.        
        </p>
        
        <p>
            It will also create the visualization part of the network containing the fluxes information for each reaction. It can be open by selecting
            the resulting model and select the option "Visualize" that appears after pressing the right button of the mouse.
        </p>
        
        <h4>Method parameters</h4>
                <dl>
                        <dt>Objective</dt>
                        <dd>ID of the compound that has to be optimized.</dd>                        
                </dl>
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